Fix bug in ClusterBatch when SR2POS not present (#775)

broadinstitute · Feb 10, 2025 · 72c15c6 · 72c15c6
1 parent 62ef705
commit 72c15c6
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/sv-pipeline/scripts/format_gatk_vcf_for_svtk.py b/src/sv-pipeline/scripts/format_gatk_vcf_for_svtk.py
@@ -153,7 +153,7 @@ def convert(record: pysam.VariantRecord,
         new_record.info['STRANDS'] = '+-'
         # END information is lost when setting POS=END, so we need to set it to SR2POS if it's available
         # Note that the END position is only important following SR breakpoint refinement in FilterBatch
-        if record.info.get('SR2POS') is not None:
+        if 'SR2POS' in record.info and record.info['SR2POS'] is not None:
             new_record.stop = record.info['SR2POS']
     elif svtype == 'BND' or svtype == 'CTX':
         new_record.stop = record.info['END2']